Difference Tables in CodonCode Aligner

Difference tables in CodonCode Aligner are a powerful tool to find and look at the differences in your contigs. A difference table shows all columns in a contig where at least one sequence differs from the consensus. In addition, totals are given for the number of differences at each position and for each sequence. Each cell in the table is linked to the underlying sequence data to enable easy verification of the differences. Difference tables can be shown for regular contigs as well as for alignments of contigs. Use the difference tables to:

  • Easily spot the differences
  • Navigate to each difference in the alignment simply by clicking on any cell in the difference table
  • Double click on a cell to show the traces at this position
  • Control which differences are displayed by using different filters (for example show only differences that have gaps at the same position in your alignment)
  • Get an overview of the differences in your contig by using the compact size that highlights differences with colors, or use the larger size for details
  • Export all of your difference tables to comma or tab seperated text files

The screenshot below shows a difference table in the contig view of CodonCode Aligner. Note how the same difference that is selected in the difference table is selected in the aligned bases panel below the difference table.

The difference table in the contig view of CodonCode Aligner

By clicking the "Change size" button above the difference table, you can see a condensed version of the difference table that highlights the differences only by color and makes it easy to spot variations:

A condensed version of the difference table

You can use the filters to show only the differences you are interested in. The example below shows only the differences that have a gap at this position of the contig:

Using the filters for the difference table to show only differences with gaps

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